aaComp: Compute the amino acid composition of a protein sequence

In dosorio/Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Compute the amino acid composition of a protein sequence

Description

This function calculates the amount of amino acids of a particular class and classified as: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charged, Basic and Acidic based on their size and R-groups using same function implemented in EMBOSS 'pepstat'. The output is a matrix with the number and percentage of amino acids of a particular class

Usage

aaComp(seq)

Arguments

seq	An amino-acid sequence

Details

Amino acids are zwitterionic molecules with an amine and a carboxyl group present in their structure. Some amino acids possess side chains with specific properties that allow grouping them in different ways. The aaComp function classifies amino acids based on their size, side chains, hydrophobicity, charge and their response to pH 7.

Value

The output is a matrix with the number and percentage of amino acids of a particular class:

• Tiny (A + C + G + S + T)

• Small (A + B + C + D + G + N + P + S + T + V)

• Aliphatic (A + I + L + V)

• Aromatic (F + H + W + Y)

• Non-polar (A + C + F + G + I + L + M + P + V + W + Y)

• Polar (D + E + H + K + N + Q + R + S + T + Z)

• Charged (B + D + E + H + K + R + Z)

• Basic (H + K + R)

• Acidic (B + D + E + Z)

Note

This function was originally written by Alan Bleasby ([e-mail]) for the EMBOSS package. Further information: http://emboss.sourceforge.net/apps/cvs/emboss/apps/pepstats.html

References

Rice, Peter, Ian Longden, and Alan Bleasby. "EMBOSS: the European molecular biology open software suite." Trends in genetics 16.6 (2000): 276-277.

Examples

# COMPARED TO PEPSTATS
# http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
# Property      Residues              Number  Mole%
# Tiny          (A+C+G+S+T)             4   19.048
# Small         (A+B+C+D+G+N+P+S+T+V)   4   19.048
# Aliphatic     (A+I+L+V)               5   23.810
# Aromatic      (F+H+W+Y)               5   23.810
# Non-polar     (A+C+F+G+I+L+M+P+V+W+Y) 11  52.381
# Polar         (D+E+H+K+N+Q+R+S+T+Z)   9   42.857
# Charged       (B+D+E+H+K+R+Z)         8   38.095
# Basic         (H+K+R)                 8   38.095
# Acidic        (B+D+E+Z)               0   00.000

## AA composition of PDB: 1D9J Cecropin Peptide
aaComp(seq= "KWKLFKKIGIGKFLHSAKKFX")

## Output
#           Number  Mole %
# Tiny           4 19.048
# Small          4 19.048
# Aliphatic      5 23.810
# Aromatic       5 23.810
# NonPolar      11 52.381
# Polar          9 42.857
# Charged        8 38.095
# Basic          8 38.095
# Acidic         0  0.000

dosorio/Peptides documentation built on Jan. 4, 2024, 2:28 p.m.